upgraded Python version to >=3.10,<4.0 in pyproject.toml, poetry.lock and databses-ci; added biotite package to dependencies #89
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| name: databases-ci | |
| on: | |
| # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming | |
| # The cookiecutter uses the "--initial-branch" flag when it runs git-init | |
| push: | |
| branches: | |
| - "main" | |
| paths: | |
| - "missense_kinase_toolkit/databases/**" | |
| pull_request: | |
| branches: | |
| - "main" | |
| paths: | |
| - "missense_kinase_toolkit/databases/**" | |
| schedule: | |
| # Weekly tests run on main by default: | |
| # Scheduled workflows run on the latest commit on the default or base branch. | |
| # (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule) | |
| - cron: "0 0 * * 0" | |
| jobs: | |
| test: | |
| name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [macOS-latest, ubuntu-latest, windows-latest] | |
| python-version: ["3.10", "3.11"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Additional info about the build | |
| shell: bash | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| # More info on options: https://github.com/marketplace/actions/provision-with-micromamba | |
| # https://github.com/mamba-org/provision-with-micromamba#migration-to-setup-micromamba%60 | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: devtools/conda-envs/test_env.yaml | |
| environment-name: test | |
| # conda-forge is the default channel now and does not need to be specified | |
| channels: conda-forge,defaults | |
| extra-specs: | | |
| python=${{ matrix.python-version }} | |
| - name: Install package | |
| # conda setup requires this special shell | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install ./missense_kinase_toolkit/databases --no-deps | |
| micromamba list | |
| - name: Run tests | |
| # conda setup requires this special shell | |
| shell: bash -l {0} | |
| run: | | |
| # run each package test suite; append to coverage file | |
| # exit immediately if a command exits with a non-zero status | |
| set -e | |
| # pytest -n auto --durations=10 -v --cov-report=xml --cov-report=term --color=yes \ | |
| pytest -v --cov-report=xml --color=yes \ | |
| --cov=missense_kinase_toolkit/databases \ | |
| missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/tests/ | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v4.0.1 | |
| with: | |
| fail_ci_if_error: false # optional (default = false) | |
| file: ./coverage.xml | |
| flags: databases # optional | |
| name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} | |
| # https://github.com/codecov/codecov-action | |
| token: ${{ secrets.CODECOV_TOKEN }} # required | |
| verbose: true # optional (default = false) |